Plant Genome Projects

Directory of Online Plant Genome Projects, Plant Genome Sequences and Plant Genomic Databases and Resources. Includes resources on Arabidopsis thaliana, Barley, Fugu, Grains, Maize and Yeast.
Biology> Genetics > Genome Projects> Plant Genome Project

- Academic Info: Human Genome Project
- Academic Info: Animal Genome Projects
- Academic Info: Plant Genome Projects

See also Academic Info: Agriculture
See also Academic Info: Biotechnology
See also Academic Info: Botany

First-Ever Complete Plant Genome Sequence Is Announced
International team reveals DNA secrets of Arabidopsis thaliana (12/14/00)

Angiosperm DNA C-Values Database Query
Royal Botanic Gardens, Kew

ARS Genome Database Resource
"...is primarily a site for communication of Plant Genome data among scientists worldwide. The medium is a set of genome databases, similar to the ones for Human genome mapping and sequencing. They include data about : plant genes, chromosome maps, DNA fingerprints, beneficial traits, and crop varieties that possess those traits. The information is contributed by the scientists who discover it, and integrated into coherent databases by teams of scientific experts in each crop."
USDA-ARS Center for Agricultural Bioinformatics - (dead link)

ChromDB - The Plant Chromatin Database
"...accurate and up-to-date information on the entire known complement of chromatin proteins in plants, including functions and molecular phylogenetic relationships, with initial emphasis on Arabidopsis and maize..."

• Beginners Guide to Chromatin - (dead link)

National Science Foundation

• Biology Home Page
  • Division of Biological Infrastructure (DBI) - (dead link)
    • Division of Plant Genome Research (PGR) - (dead link)
      • Net Center for Plant Genomics - (dead link)
        "...this resource will facilitate the interaction between members of Plant Genome projects and broaden the participation of the community in sharing the resources generated by these projects."

PlantsP: Functional Genomics of Plant Phosphorylation
"The DB Search function is the entry point to information about specific genes, protein motif/domain diagrams, exon/intron digrams, and BLAST database searches of both PlantsP, Arabidopsis genome, and all plant sequences."
"A distributed project investigating the biology of protein kinases and phosphatases in Arabidopsis thaliana and other plants. Funded by the plant genome program of the National Science Foundation (DBI-9975808)."

PtantsT: Functional Genomics of Plant Transporters
"PlantsT is part of the Plant Genome Program for the National Science Foundation. This database is a central site for the study of the uptake and translocation of mineral nutrients in plants. In spite of recent advances in identifying genes involved in nutrient transport, the systems that control acquisition of individual nutrients remain largely unknown. The major objective of this project is to identify gene networks that control uptake and accumulation of a wide array of plant nutrients and toxic metals."

Realizing the Potential of Plant Genomics:
From Model Systems to the Understanding of Diversity
Mission Statement: "To exploit the revolution in plant genomics by understanding the function of all plant genes within their cellular, organismal and evolutionary context and to create an information structure to coordinate, integrate, analyze and make accessible knowledge about plant biology."
National Science Foundation report

U.S. Dept. of Agriculture - Plant Genome Data and Information Center
Sections include: Full-Text Digitized Plant Books and Journals ; Access to Literature and Research ; Experimental Resources ; Biodiversity ; Educational Resources ; Biotechnology Resources.

• GrainGenes
  A Small Grains and Sugercane Database
  "...is a compilation of molecular and phenotypic information on wheat, barley, rye, oats and sugarcane."

Arabidopsis

The Arabidopsis cDNA Sequence Analysis Project - (dead link)

Arabidonsis Genome Initiative (AGI) - (dead link) "...the genome sequencing is now completed at the end of 2000."

• First-Ever Complete Plant Genome Sequence Is Announced
  International team reveals DNA secrets of Arabidopsis thaliana (12/14/00)

Center for Eukaryotic Structural Genomics
"...is a collaborative effort to elucidate the three-dimensional structure of many of the proteins encoded by the Arabidopsis thaliana genome. Starting with characterized cDNA clones, recombinant protein is produced and subsequently purified. The three dimensional structure of the proteins is then determined via either X-ray crystallography or nuclear magnetic resonance (NMR). All solved structures will be promptly placed in public databases including the Protein Data Bank (PDB) and BioMagResBank (BMRB)."
- University of Wisconsin-Madison - Dept. of Biochemistry

PlantsP: Functional Genomics of Plant Phosphorylation
"The DB Search function is the entry point to information about specific genes, protein motif/domain diagrams, exon/intron digrams, and BLAST database searches of both PlantsP, Arabidopsis genome, and all plant sequences."
"A distributed project investigating the biology of protein kinases and phosphatases in Arabidopsis thaliana and other plants. Funded by the plant genome program of the National Science Foundation (DBI-9975808)."

Proteins of Arabidopsis Thaliana (PAT) - (dead link)
"...is a project to predict, using homology modeling, the three dimensional structures of proteins encoded in Arabidopsis thaliana genome. We combined the results from BLAST-WU, PSI-BLAST, 123D+, COILS, TMHMM, SignalP and organized them in the relational database with web-based GUI for simplified access."

TAIR - The Arabidopsis Information Resource - (dead link)
"provides a comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant. TAIR consists of a searchable relational database, which includes many different datatypes."
A collaboration between the Carnegie Institution of Washington Department of Plant Biology, Stanford, California, and the National Center for Genome Resources (NCGR), Santa Fe, New Mexico.

Barley

Barley EST Project - (dead link)
"The Barley HV__Ea EST collection is composed of 13 separate EST libraries."
Clemson University - Genomics Institute

Fugu

DOE Joint Genome Institute (JGI)
Operated by The University of California for The US Department of Energy

• Fugu Genome Project
  "...An international research consortium has taken a substantial short cut to the biologically important information embedded in the human genome with the completion of a draft sequence of the genome of the Japanese pufferfish Fugu rubripes."
  • Data Release - (dead link) (10/26/01)
    "...the draft assembly of the Fugu rubripes genome, as well as the raw sequencing data that contributed to the assembly, is being made available by the Fugu Genome Consortium before scientific publication."

Grains

GrainGenes
A Small Grains and Sugercane Database
"...is a compilation of molecular and phenotypic information on wheat, barley, rye, oats and sugarcane."

Gramene: A Comprehensive Mapping Resource for Grains
"...to create a curated, open-source, Web-accessible data resource for comparative genome analysis in the grasses. Data formerly in RiceGenes is now integrated in Gramene. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations."

Maize

Maize Mapping Project
"An Integrated Genetic and Physical Map for Maize, to provide the draft foundation for complete or partial sequencing of this most important US crop, is approximately half complete. The target is to define contiguous, overlapping physical pieces (contigs) of the maize genome to the greatest extent possible."
Sections include: Integrated Map ; Maps ; Bio-Informatics ; Resources ; Education/Outreach ; About ; Data Access.
Collaboration of researchers at the University of Missouri-Columbia, Clemson University, and the University of Georgia.

Maize Targeted Mutagenesis Database (MTMDB)
"...is a transposon library in maize for the purpose of targeted selection of gene knockouts. It currently contains 43,776 DNA samples from F1 insertion plants and 43,776 F2 progeny...The final database is expected to include information on over 80,000 Mu insertion mutant alleles with recessive or dominant phenotypes."

__________

Yeast

Comprehensive Yeast Genome Database
"...aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis."
- Munich Information Center for Protein Sequences

Ares Lab Yeast Intron Database
"This site contains information about the spliceosomal introns of the yeast Saccharomyces cerevisiae...we include expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. These data are displayed on each intron page for browsing and can be downloaded for other types of analysis."
By Leslie Grate, Angela Telerski, Tyson Clark, Ross Centers and Manny Ares, University of California, Santa Cruz.

Saccharomyces Genome Deletion Project
"The purpose of this page is to communicate protocols, methods and information about the project and to provide access to the Yeast Deletion Database (consortium members only)...The goal of the Saccharomyces Genome Deletion Project is to generate as complete a set as possible of yeast deletion strains with the overall goal of assigning function to the ORFs through phenotypic analysis of the mutants."

• Yeast Deletion Strains from Research Genetics and American Type Culture Collection - (dead link)

Proceed to:

- Academic Info: Human Genome Project
- Academic Info: Animal Genome Projects
- Academic Info: Plant Genome Projects

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